adjustP2                package:CALIB                R Documentation

_A_d_j_u_s_t _m_o_d_e_l _p_a_r_a_m_e_t_e_r _P_2

_D_e_s_c_r_i_p_t_i_o_n:

     Adjust the calibration model parameter P2 according to the
     measured intensities of all clones spotted on the array.

_U_s_a_g_e:

     adjustP2(RG, parameter, arrayindex = arrayindex, colorindex = colorindex)

_A_r_g_u_m_e_n_t_s:

      RG: an 'RGList' object.

parameter: a 'ParameterList' object. 

arrayindex: integer vector specifying the index of the arrays of whose 
          the parameter P2 needed to be adjusted. 

colorindex: integer vector specifying which color needed to be
          adjusted.

_D_e_t_a_i_l_s:

     'RG' is an 'RGList_CALIB' object which contains all the
     experimental data.  'parameter' is the return result of function
     'estimateParameter.' 'arrayindex' is an integer vector. It gives
     the index of the arrays whose P2 is  needed to be adjusted.
     'colorindex' is an integer vector. It gives the color needed to be
     adjusted. '1' means red P2 and '2' means green P2.

_V_a_l_u_e:

     It returns a 'ParameterList' object with a adjusted P2 compared to
     the input argument 'parameter'.

_N_o_t_e:

     The user should decide on which array and which color the
     adjustment is needed. Therefore it is important to specify the
     right array index and color index. There is no check on this in
     the function.

_A_u_t_h_o_r(_s):

     Hui Zhao

_E_x_a_m_p_l_e_s:

     # load data: RG and parameter:
     data(RG)
     data(parameter)

     # adjust P2
     parameter_new <- adjustP2(RG,parameter,arrayindex=c(1,2),colorindex=c(2,2))

